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  • GATK UnifiedGenotyper SNP calling with Agilent 50Mb target enrichment

    I am trying (and failing) to call SNPs using a reference file (.BED) specifically for the Agilent 50Mb Sureselect enrichment sequencing. I am using the GATK UnifiedGenotyper with the following commands. Any ideas? Thanks!

    java -jar ~/Sting/dist/GenomeAnalysisTK.jar \
    -R ~/Documents/refFASTA/SureSelect_All_Exon_50mb.bed \
    -l INFO \
    -T UnifiedGenotyper \
    -I ~/Documents/next_gen/sorted.N.dupesremoved.recali.bam \
    -o ~/Documents/SNP/N_AgilentSS_50MB_gatk.vcf \
    -stand_call_conf 50.0 \
    -stand_emit_conf 10.0 \
    -dcov 150

  • #2
    solved

    The above code should have contained the argument "-L" for the interval list (bed) file and also a "-R" for the reference fasta file!

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